#perl perl_removeambiguous_removeX.pl /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/files/reference/hapmapfiles/hapmap3.tped.fws.norm.tped /data1/bsi/bioinf_int/s106381.borawork/data_HTHGU/illumina1/MayoGAP/mayogap_emerge/raw/clean/beagle/run_beagle/beagle_mainrun/workflow/files/reference/hapmapfiles/hapmap3_sample_run.tped
$input_file = $ARGV[0];
chomp($input_file);
$output_file = $ARGV[1];
chomp($output_file);
open BUFF,"<$input_file" or die "Not able to open the file $input_file";
open(WRBUFF,">$output_file");
while($line = <BUFF>)
{	
	chomp($line);
	if($line =~ m/^X/ || $line =~ m/ A T/ || $line =~ m/ G C/)
	{
	}
	else
	{	
		print WRBUFF $line."\n";
	}

}
